I know this will shut down all electronics but will it have any affect on the water in streams or lakes?
The pervasive myth that an EMP strike will shut down all electronics is not supported by science or real world testing.
What do you mean by "affect on water in streams or lakes"? Like will it contaminate it? No, EMP won't affect the water but the second and third order affects of a successful and damaging strike could result in contaminated water.